i am using marvin 5.3.4. i am having trouble with atom numbering , for subsquent calculation of RMSD with the pdb structure.
i wish to know how to reorder the default atom numbering??
pleaseeeeeeee help, i have a submission to make.
You can use the manual mapping function:
-move the mouse over any atom
-type m and the number you wish to add to the atom
-repeat this 2 steps over every atom you'd like to number
To remove atom map, type: m0
If you mean the inherent atom numbering rather than atom mapping, the atoms are numbered according to their order of appearance in the code (SMILES, MOL, MRV) that describes the drawing. To renumber the atoms, you need to rearrange the order of atoms (taking care to make sure the bonds stay in the same place).
Alternatively, you can redraw the molecule; Marvin will number atoms according to the sequence in which you place them on the canvas.
Yes, this is also a solution; thank you Bob.